AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ipurR_tpal_opreg_100.orf -g0.528 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0284 104 T. pallidum predicted coding region TP0284 #2 TP0289 22 T. pallidum predicted coding region TP0289 #3 TP0290 54 conserved hypothetical protein #4 TP0291 36 T. pallidum predicted coding region TP0291 #5 TP0329 117 serine hydroxymethyltransferase (glyA) #6 TP0694 159 5,10-methenyltetrahydrofolate synthetase, putative #7 TP0695 87 phosphoribosylglycinamide formyltransferase, putative Motif number 1 ATTCTTTTTCTCACTCGGTTGAGTGATCTTCG 1 35 1 TCACTGGTTA 0.748363 -70 AACTTTAAAAGCACAGCCCCGAAGATCACTCA 1 54 0 GCACACCCCA 0.940083 -51 TGGTGCAGTACGCTGAAGTAAT 2 7 0 GCAGTCGCTA 0.890433 -16 TTTTGGGTGTGCACTTGTTCAAGTTCAGAGGT 3 26 1 GCACTGTTCA 0.825104 -29 CCCTAAAAAAGCACTGCCCTCT 4 1 0 GCACTCCCTT 0.975515 -36 CCCCTGTTACGCACGACGGGTATCGGGCATGC 5 20 1 GCACGCGGGA 0.951406 -98 GGCATGCGGCGCGCGGCGTTTTGTCCATTCTT 5 45 1 GCGCGCGTTT 0.918006 -73 CGGTACTTTAGCACGCGGCTGTGGTGTGCGCT 6 37 0 GCACGGGCTT 0.992581 -123 TAAAGTACCGTCACGGGCCCTTCGTTACAGCC 6 59 1 TCACGGCCCT 0.935203 -101 CAAAGACACATCACGTCTTCTTTTCGTTAGGG 6 107 1 TCACGCTTCT 0.80003 -53 GCGTCGTCCTGCACGTCCCTAACGAAAAGAAG 6 123 0 GCACGCCCTA 0.994545 -37 GGGACGTGCAGGACGACGCCGACACCACCCAT 6 136 1 GGACGCGCCA 0.966453 -24 CTTGGTGCATGCACGTGTGTGATTAGAATGGA 7 22 0 GCACGGTGTA 0.929773 -66 TGGGAAGATAGCACGGCGCTGTCCTCTTGGTG 7 47 0 GCACGCGCTT 0.995758 -41 ***** **** * Masking position 3 Map Score: 17.238 Number of sites scoring better than the average of aligned sites = 1659 Number in coding regions = 1536 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 ATGTGATGATTCTTTTTCTCACTCGGTTGA 1 27 1 TCTTTTTCTC 0.896087 -78 GCGATCTTCCTTTTCCCTAAAAAA 4 23 0 TCTTCCTTTT 0.95715 -14 GCGCGGCGTTTTGTCCATTCTTTGCGCTAG 5 55 1 TTGTCCATTC 0.902021 -63 GTTTTTCTCTCCTCAGGTAGG 5 107 0 TTTTTCTCTC 0.896087 -11 ACACATCACGTCTTCTTTTCGTTAGGGACG 6 112 1 TCTTCTTTTC 0.979157 -48 TGCCTTATTCCTCCATTCTAATCACACA 7 9 1 TCCTCCATTC 0.984154 -79 GTGTTTTCATCCTCCTTTCTGGGAAGATA 7 69 0 TCCTCCTTTC 0.993044 -19 ********** Masking position 4 Map Score: 5.346 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 231 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 GAAAAAGAATCATCACATACTCAGCTCATGCA 1 13 0 CACACATACC 0.98181 -92 TGAACTTTAAAAGCACAGCCCCGAAGATCACT 1 56 0 AACACAGCCC 0.982304 -49 ACCCAAAAAACAACACGGCAACT 3 2 0 CACACGGCAC 0.969169 -53 AAACGCCGCGCGCCGCATGCCCGATACCCGTC 5 34 0 CGCGCATGCC 0.973456 -84 CTGCAGCGCACACCACAGCCGCGTGCTAAAGT 6 33 1 CACACAGCCC 0.998237 -127 GCTAAAGTACCGTCACGGGCCCTTCGTTACAG 6 57 1 CGCACGGGCC 0.995302 -103 ACGGGCCCTTCGTTACAGCCACCCTACGATAT 6 71 1 CGTACAGCCC 0.986201 -89 CTACGATATCCACCAAAGACACATCACGTCTT 6 94 1 CACAAAGACC 0.964129 -66 ACGTGCAGGACGACGCCGACACCACCCATAC 6 139 1 CGCGCCGACC 0.981512 -21 ** ******* * Masking position 12 Map Score: 14.4058 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 366 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 CATGAGCTGAGTATGTGATGATTCTTTTTC 1 15 1 GTATGTGATG 0.894937 -90 AGTTGCCGTGTTGTTTTTTGGGT 3 4 1 TGCCGTGTTG 0.802559 -51 CGGGTATCGGGCATGCGGCGCGCGGCGTTT 5 36 1 GCATGCGGCG 0.959283 -82 CACCTCTTTATTCTGCAGCGCACACCACAG 6 21 1 TTCTGCAGCG 0.848224 -139 TTTAGCACGCGGCTGTGGTGTGCGCTGCAG 6 33 0 GGCTGTGGTG 0.990802 -127 GTAACGAAGGGCCCGTGACGGTACTTTAGC 6 57 0 GCCCGTGACG 0.975549 -103 ATCGTAGGGTGGCTGTAACGAAGGGCCCGT 6 71 0 GGCTGTAACG 0.952841 -89 GACGTGATGTGTCTTTGGTGGATATCGTAG 6 94 0 GTCTTTGGTG 0.897528 -66 TATGGGTGGTGTCGGCGTCGTCCTGCACGT 6 139 0 GTCGGCGTCG 0.9377 -21 ********** Masking position 10 Map Score: 4.38894 Number of sites scoring better than the average of aligned sites = 1361 Number in coding regions = 1248 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 GCTTTTAAAGTTCAGAAAAGTTTTGAGCAA 1 74 1 TTCAGAAAAG 0.891903 -31 CAGAAAAGTTTTGAGCAAGGTTCTCCTGC 1 86 1 TTGAGCAAGG 0.938279 -19 AGTGCTTTTTTAGGGAAAAGGAAGATCGC 4 18 1 TAGGGAAAAG 0.971978 -19 GCTCTGTTTCTAGCGCAAAGAATGGACAAA 5 64 0 TAGCGCAAAG 0.987194 -54 AGGGTGGCTGTAACGAAGGGCCCGTGACGG 6 66 0 TAACGAAGGG 0.92598 -94 TGCACGTCCCTAACGAAAAGAAGACGTGAT 6 116 0 TAACGAAAAG 0.976341 -44 ********** Masking position 7 Map Score: 1.70653 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 80 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ********** No masking Map Score: -1.39676e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: -1.39676e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: -1.39676e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0